rs10811771

chr9-22770887-A-Gchr9-22770887-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038977.1(LINC01239):n.524+47457A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,834 control chromosomes in the GnomAD database, including 8,236 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (8236 hom., cov: 31)
• Consequence: LINC01239 NR_038977.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

LINC01239 (HGNC:49796): (long intergenic non-protein coding RNA 1239)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01239	NR_038977.1	n.524+47457A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01239	ENST00000436786.1	n.524+47457A>G		intron_variant, non_coding_transcript_variant		2
	ENST00000640003.1	n.559-5611T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47141 AN: 151716 Hom.: 8235 Cov.: 31

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.321

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.311 AC: 47145 AN: 151834 Hom.: 8236 Cov.: 31 AF XY: 0.311 AC XY: 23060 AN XY: 74194

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.438

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.317

Alfa AF: 0.360 Hom.: 9855

Bravo AF: 0.313

Asia WGS AF: 0.260 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.67
Dann	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10811771; hg19: chr9-22770886;